FastqDownsampler: The FastqDownsampler class

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Package: aroma.seq
Class FastqDownsampler

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--FastqDownsampler

Directly known subclasses:

public static class FastqDownsampler
extends AromaSeqTransform

...

Usage

FastqDownsampler(dataSet=NULL, subset=1e+06, seed=NULL, ...)

Arguments

dataSet	An FastqDataSet.
subset	An integer specifying the total number of reads to sample, or a double specifying the fraction of total number of reads to sample.
seed	An (optional) integer specifying the random seed to be set before sampling indices. The random seed is set to its original state when exiting. If NULL, it is not set.
...	Additional arguments passed to AromaSeqTransform.

Fields and Methods

Methods:

	process	-

Methods inherited from AromaSeqTransform:
as.character, findFilesTodo, getAcronym, getAsteriskTags, getFlavor, getFullName, getInputDataSet, getName, getOptionalArguments, getOrganism, getOutputDataSet, getParameters, getPath, getRootPath, getTags, isDone, length, process, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, findRspReportTemplate, asThis

Author(s)

Henrik Bengtsson

See Also

Internally, the FastqSampler method is used.

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.